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K C Holmes

Publications and source records attributed to K C Holmes.

At least 19 recordsLinked to original sources
PubMed2000

The structural basis of muscle contraction.

The myosin cross-bridge exists in two conformations, which differ in the orientation of a long lever arm. Since the lever arm undergoes a 60 degree rotation between the two conformations, which would lead to a displacement of the myosin filament of about 11 nm, the transition between these two states has been associated with the elementary 'power stroke' of muscle. Moreover, this rotation is coupled with changes in the active site (CLOSED to OPEN), which probably enable phosphate release. The transition CLOSED to OPEN appears to be brought about by actin binding. However, kinetics shows that the binding of myosin to actin is a two-step process which affects both ATP and ADP affinity and vice versa. The structural basis of these effects is only partially explained by the presently known conformers of myosin. Therefore, additional states of the myosin cross-bridge should exist. Indeed, cryoelectron microscopy has revealed other angles of the lever arm induced by ADP binding to a smooth muscle actin-myosin complex.

Actins↗
PubMed1999

Structural biology.

Protein crystallography has become a major technique for understanding cellular processes. This has come about through great advances in the technology of data collection and interpretation, particularly the use of synchrotron radiation. The ability to express eukaryotic genes in Escherichia coli is also important. Analysis of known structures shows that all proteins are built from about 1000 primeval folds. The collection of all primeval folds provides a basis for predicting structure from sequence. At present about 450 are known. Of the presently sequenced genomes only a fraction can be related to known proteins on the basis of sequence alone. Attempts are being made to determine all (or as many as possible) of the structures from some bacterial genomes in the expectation that structure will point to function more reliably than does sequence. Membrane proteins present a special problem. The next 20 years may see the experimental determination of another 40,000 protein structures. This will make considerable demands on synchrotron sources and will require many more biochemists than are currently available. The availability of massive structure databases will alter the way biochemistry is done.

Crystallography, X-Ray↗
PubMed1999

Role of the salt-bridge between switch-1 and switch-2 of Dictyostelium myosin.

Motifs N2 and N3, also referred to as switch-1 and switch-2, form part of the active site of molecular motors such as myosins and kinesins. In the case of myosin, N3 is thought to act as a gamma-phosphate sensor and moves almost 6 A relative to N2 during the catalysed turnover of ATP, opening and closing the active site surrounding the gamma-phosphate. The closed form seems to be necessary for hydrolysis and is stabilised by the formation of a salt-bridge between an arginine residue in N2 and a glutamate residue in N3. We examined the role of this salt-bridge in Dictyostelium discoideum myosin. Myosin motor domains with mutations E459R or R238E, that block salt-bridge formation, show defects in nucleotide-binding, reduced rates of ATP hydrolysis and a tenfold reduction in actin affinity. Inversion of the salt-bridge in double-mutant M765-IS eliminates most of the defects observed for the single mutants. With the exception of a 2,500-fold higher KMvalue for ATP, the double-mutant displayed enzymatic and functional properties very similar to those of the wild-type protein. Our results reveal that, independent of its orientation, the salt-bridge is required to support efficient ATP hydrolysis, normal communication between different functional regions of the myosin head, and motor function.

Adenosine Diphosphate↗
PubMed1999

Structural mechanism of muscle contraction.

X-ray crystallography shows the myosin cross-bridge to exist in two conformations, the beginning and end of the "power stroke." A long lever-arm undergoes a 60 degrees to 70 degrees rotation between the two states. This rotation is coupled with changes in the active site (OPEN to CLOSED) and phosphate release. Actin binding mediates the transition from CLOSED to OPEN. Kinetics shows that the binding of myosin to actin is a two-step process which affects ATP and ADP affinity. The structural basis of these effects is not explained by the presently known conformers of myosin. Therefore, other states of the myosin cross-bridge must exist. Moreover, cryoelectronmicroscopy has revealed other angles of the cross-bridge lever arm induced by ADP binding. These structural states are presently being characterized by site-directed mutagenesis coupled with kinetic analysis.

Actins↗
PubMed1999

Medical student database development: a model for record management in a multi-departmental setting.

Student records flow through medical school offices at a rapid rate. Much of this data is often tracked on paper, spread across multiple departments. The Medical Student Informatics Group at the University of Utah School of Medicine identified offices and organizations documenting student information. We assessed departmental needs, identified records, and researched database software available within the private sector and academic community. Although a host of database applications exist, few publications discuss database models for storage and retrieval of student records. We developed and deployed an Internet based application to meet current requirements, and allow for future expandability. During a test period, users were polled regarding utility, security, stability, ease of use, data accuracy, and potential project expansion. Feedback demonstrated widespread approval, and considerable interest in additional feature development. This experience suggests that many medical schools would benefit from centralized database management of student records.

Consumer Behavior↗
PubMed1998

A molecular model for muscle contraction.

The molecular mechanism of muscle contraction has been elucidated by a combination of electron microscopy, biochemistry and X-ray diffraction from fibres and crystals. Protein crystallography provided the essential molecular anatomy for understanding this problem. Synchrotron radiation has played a crucial role.

Animals↗
PubMed1998

Muscle contraction.

Understanding muscle contraction goes to the heart of one of the fundamental questions posed by classical philosophy, namely the nature of the pi nu epsilon upsilon mu alpha psi nu chi iota kappa omicron nu. The nature of 'understanding' has altered greatly during the last two millenia, particularly in response to the development of the concept of energy. Moreover, understanding contraction depends on understanding muscle structure. Galen was the first to make a detailed anatomical examination of the mode of action of muscles and recognized the heart as a muscle, but this line of research was not pursued until Leonardo da Vinci rediscovered it 1400 years later. Vesalius used the phrase Machina Carnis, but it was first Descartes who proposed a neuromuscular machine. However, the level of understanding of the physiology of muscle depends critically on the resolution of the available anatomy. Radical new insight was provided by electron microscopy. But an understanding at a physicochemical level is only possible if the structures of the components are known at atomic resolution. These have become known in the last five years and have led to dramatic progress. The present level of understanding of muscle is a physicochemical explanation of how the hydrolysis of ATP by the component proteins actin and myosin leads to movement.

Actins↗
PubMed1997

The swinging lever-arm hypothesis of muscle contraction.

The molecular mechanism of muscle contraction is a problem that has exercised biophysicists and biochemists for many years. The common view of the mechanism is embodied in the 'cross-bridge hypothesis', in which the relative sliding of thick (myosin) and thin (actin) filaments in cross-striated muscle is brought about by the 'cross-bridges', parts of the myosin molecules which protrude from the thick filaments and interact cyclically with the actin filaments, transporting them by a rowing action that is powered by the hydrolysis of ATP. This hypothesis is, however, rather vague on the molecular details of cross-bridge movement and, in the light of the recently determined crystal structures of myosin and actin, it has evolved into the more precise 'swinging lever-arm hypothesis'.

Actins↗
PubMed1996

Muscle proteins--their actions and interactions.

Muscle contracts by the myosin cross-bridges "rowing' the actin filaments past the myosin filaments. In the past year many structural details of this mechanism have become clear. Structural studies indicate distinct states for myosin S1 in the rigor, ATP or "down' conformation and in the products complex (ADP.Pi) or "up' to state. Crystallographic studies substantiate this classification and yield details of the transformation. The isomerization "up' to "down' is the power stroke of muscle. This consists in the main of large changes of angle of the "lever arm' (at the distal part of the myosin head) which can account for an 11 nm power stroke.

Actomyosin↗
PubMed1995

An atomic model of the unregulated thin filament obtained by X-ray fiber diffraction on oriented actin-tropomyosin gels.

We present a model of the actin-tropomyosin complex in which the radial and azimuthal position of tropomyosin was adjusted to fit the X-ray fiber diffraction patterns from oriented actin-tropomyosin gels at a resolution of 1/8 A-1. We used the recently published atomic F-actin model for the calculations. The atomic model of tropomyosin was obtained by model-building a coiled coiled-coil structure from the tropomyosin sequence. The resulting atomic model is strongly preferred and shows strong electrostatic interactions between charged side-chains of tropomyosin residues and actin residues in subdomain 3 and subdomain 4. Furthermore, calculations of enthalpies based upon electrostatic interactions indicate that there is a favored rotational position of the tropomyosin core at the calculated azimuthal and radial position given by the X-ray refinement. Rotations of the tropomyosin strand out of this position turn strongly attractive electrostatic interactions into repulsive forces. The resulting binding radius of 39 A and the determined azimuthal position of tropomyosin are in good agreement with electron microscopy reconstructions and neutron diffraction experiments. Furthermore, the calculated position of tropomyosin would still partly block the rigor interaction of myosin cross-bridges with actin, whereas it very likely allows undisturbed binding of the cross-bridges in a weak binding state.

Actins↗
PubMed1995

Normal modes as refinement parameters for the F-actin model.

The slow normal modes of G-actin were used as structural parameters to refine the F-actin model against 8-A resolution x-ray fiber diffraction data. The slowest frequency normal modes of G-actin pertain to collective rearrangements of domains, motions that are characterized by correlation lengths on the order of the resolution of the fiber diffraction data. Using a small number of normal mode degrees of freedom (< or = 12) improved the fit to the data significantly. The refined model of F-actin shows that the nucleotide binding cleft has narrowed and that the DNase I binding loop has twisted to a lower radius, consistent with other refinement techniques and electron microscopy data. The methodology of a normal mode refinement is described, and the results, as applied to actin, are detailed.

Actins↗
PubMed1995

The actin fold.

X-ray structure analysis of actin and of the NH2-terminal domain of the heat-shock cognate protein Hsc70 has revealed an unexpected extensive structural similarity between these two molecules. Despite the absence of significant similarity of their amino acid sequences, both proteins share the same core architecture and a common nucleotide binding site resembling the structure of hexokinase. All three are ATPases or kinases and bind ATP in association with Mg2+ or Ca2+. The common fold consists of two alpha/beta domains, which are connected by a putative hinge with an ATP-binding site situated between the domains. Each domain contains a five-stranded beta-sheet of identical topology, which suggests that the molecules may have evolved by gene duplication. From a comparison of the three aligned structures, a fingerprint sequence of the adenine nucleotide binding pocket was derived, which predicted that members of the glycerol kinase family should also have a similar fold of their nucleotide binding domain. This was later confirmed when the X-ray structure was published. Data base search with a refined consensus sequence has retrieved other sugar kinases, as well as the prokaryotic cell cycle proteins FtsA, MreB, and StbA, and two Escherichia coli phosphatases. These proteins are predicted to possess a structure similar to actin in the common core region. As exemplified for actin, Hsc70, and glycerol kinase, the diversity of biological function is provided by the polymorphism of the loops joining the beta-strands and helices in the core region and by inserted domains that show high variability.

Actins↗